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We went to the Maldives from Sweden this summer. I checked out prices of regular flights and it was more expensive to just fly in then to buy a package from a tour operator so when it comes to the Maldives I would say that tour operators is the cheap option.
However - if you are nearby anyway (India?) it may be different.

So the answer is: yes, you can, if you really want to. In practice, though, it makes little sense.
The Maldives are explicitly set up to discourage independent travellers. The only places you can go without a permit are the capital Male, which is pint-sized and notably lacking in all the things that make the Maldives great (white sand beaches, clear ...

The only way to fly there cheaper is to string separate flights together.
I.e. from Australia it's possible to get there for just over £500 GBP return by flying:
Melbourne→Malaysia • Malaysia→Sri Lanka • Sri Lanka→Male.
Obviously, this is going to be a headache, and the you have the hotel costs. I'm sure the answer above is on the money. So to speak.

Condor fly to Malé from Frankfurt (am Main) and has pretty decent rates. So if you fly from Europe, then it's cheaper to get there than on most packages I've seen in catalogues.
Still, I would also like to ask the for your experience what to do next, when I get there.

I planned my trip to Sri Lanka without agencies. I found tickets with Condor Airlines with 1 stop in the Maldives. I have never been before at the Maldives, so I decided to stop for 5 days in Malé. So I have 5 days to explore Maldives as an independent traveler.
I can tell you, that there is no problem for you to plan your trip to Maldives without agency, ...